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accession-icon GSE873
Muscle, normal extraocular, profile
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Molecular definition of human extraocular muscles (EOM). Human EOM were compared with limb (quadriceps femoris) muscle.

Publication Title

Definition of the unique human extraocular muscle allotype by expression profiling.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon E-MEXP-891
Transcription profiling by array of mammary gland from Akt1 knock-out mice
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430A Array (moe430a)

Description

A comparison of gene expression in the mammary gland of lactating mice at day 9 after parturition between Akt -/- and wildtype individuals.

Publication Title

Isoform-specific requirement for Akt1 in the developmental regulation of cellular metabolism during lactation.

Sample Metadata Fields

Sex, Age, Specimen part, Subject

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accession-icon GSE54652
A circadian gene expression atlas in mammals: Implications for biology and medicine
  • organism-icon Mus musculus
  • sample-icon 288 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

A circadian gene expression atlas in mammals: implications for biology and medicine.

Sample Metadata Fields

Specimen part

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accession-icon GSE26212
The effects of EBV transformation on gene expression and methylation levels
  • organism-icon Homo sapiens
  • sample-icon 82 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V3.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

The effects of EBV transformation on gene expression levels and methylation profiles.

Sample Metadata Fields

Sex, Specimen part, Subject

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accession-icon GSE58942
The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines
  • organism-icon Homo sapiens
  • sample-icon 187 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V3.0 expression beadchip

Description

Epstein-Barr virus (EBV) transformed lymphoblastoid cell lines (LCLs) are a widely used renewable resource for functional genomic studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. However, the extent to which LCLs are a faithful model system is relatively unknown. We have previously shown that gene expression profiles of newly established LCLs maintain a strong individual component. Here, we extend our study to investigate the effect of freeze-thaw cycles on gene expression patterns in mature LCLs, especially in the context of inter-individual variation in gene regulation. We found a profound difference in the gene expression profiles of newly established and mature LCLs. Once newly established LCLs undergo a freeze-thaw cycle, the individual specific gene expression signatures become much less pronounced as the gene regulatory programs in LCLs from different individuals converge to a more uniform profile, which reflects a mature transformed B cell phenotype. As expected, previously identified eQTLs are enriched among the relatively few genes whose regulations in mature LCLs maintain marked individual signatures. We thus conclude that findings and insight drawn from gene regulatory studies in mature LCLs are generally not affected by artificial nature of the LCL model system and are likely to faithfully reflect regulatory interactions in primary tissues. However, our data indicate that many aspects of primary B cell biology cannot be observed and studied in mature LCL cultures.

Publication Title

The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE25507
Autism and increased paternal age related changes in global levels of gene expression regulation
  • organism-icon Homo sapiens
  • sample-icon 146 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

A causal role of mutations in genes encoding for multiple general transcription factors in neurodevelopmental disorders including autism suggested that alterations at the global level of gene expression regulation might also relate to disease risk in sporadic cases of autism. This premise can be tested by evaluating for global changes in the overall distribution of gene expression levels. For instance, in mice, we recently showed that variability in hippocampal-dependent behaviors was associated with variability in the pattern of the overall distribution of gene expression levels, as assessed by variance in the distribution of gene expression levels in the hippocampus. We hypothesized that a similar change in the variance in gene expression levels might be found in children with autism. Gene expression microarrays covering greater than 47,000 unique RNA transcripts were done on purified RNA from peripheral blood lymphocytes of children with autism (n=82) and controls (n=64). The variance in the distribution of gene expression levels from each microarray was compared between groups of children. Also tested was whether a risk factor for autism, increased paternal age, was associated with variance in the overall distribution of gene expression levels. A decrease in the variance in the distribution of gene expression levels in peripheral blood lymphocytes (PBL) was associated with the diagnosis of autism and a risk factor for autism, increased paternal age. Traditional approaches to microarray analysis of gene expression suggested a possible mechanism for decreased variance in gene expression. Gene expression pathways involved in transcriptional regulation were down-regulated in the blood of children with autism and children of older fathers. Thus, results from global and gene specific approaches to studying microarray data were complimentary and supported the hypothesis that alterations at the global level of gene expression regulation are related to autism and increased paternal age. Regulation of transcription, thus, represents a possible point of convergence for multiple etiologies of autism and other neurodevelopmental disorders.

Publication Title

Autism and increased paternal age related changes in global levels of gene expression regulation.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE16147
Microarray Expression Analysis of SIV infection of Sooty Mangabeys
  • organism-icon Macaca mulatta, Cercocebus atys
  • sample-icon 61 Downloadable Samples
  • Technology Badge Icon Affymetrix Rhesus Macaque Genome Array (rhesus)

Description

Natural SIV infection of sooty mangabeys (SMs) does not progress to disease despite chronic virus replication. In contrast to pathogenic SIV infection of rhesus macaques (RMs), chronic SIV infection of SMs is characterized by low immune activation. To elucidate the mechanisms underlying this phenotype, we longitudinally assessed host gene expression in SIV-infected SMs and RMs. We found that acute SIV infection of SMs is consistently associated with a robust innate immune response, including widespread up-regulation of interferon-stimulated genes (ISGs). Our findings indicate that active immune regulatory mechanisms, rather than intrinsically attenuated innate immune responses, underlie the low immuneactivation of chronically SIV-infected SMs.

Publication Title

Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE6514
Gene expression in the mouse brain during spontaneous sleep and prolonged wakefulness
  • organism-icon Mus musculus
  • sample-icon 90 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

These studies address temporal changes in gene expression during spontaneous sleep and extended wakefulness in the mouse cerebral cortex, a neuronal target for processes that control sleep; and the hypothalamus, an important site of sleep regulatory processes. We determined these changes by comparing expression in sleeping animals sacrificed at different times during the lights on period, to that in animals sleep deprived and sacrificed at the same diurnal time.

Publication Title

Macromolecule biosynthesis: a key function of sleep.

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE41870
CD4+ and CD8+ T cells responding to LCMV-Armstrong or LCMV-Clone 13
  • organism-icon Mus musculus
  • sample-icon 79 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Network analysis reveals centrally connected genes and pathways involved in CD8+ T cell exhaustion versus memory.

Sample Metadata Fields

Specimen part

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accession-icon GSE61089
Mouse and rat cells and tissues
  • organism-icon Mus musculus, Rattus norvegicus
  • sample-icon 79 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Divergence of RNA localization between rat and mouse neurons reveals the potential for rapid brain evolution.

Sample Metadata Fields

Age, Specimen part

View Samples
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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

fund-icon Fund the CCDL

Developed by the Childhood Cancer Data Lab

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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